pdbaln fails to read one PDB in a set of PDBs, unhelpful error message

[Matthew Watson]

HI bio3d users, I am having an issue with a PDB file not being correctly read by bio3d - I have a folder continaing three PDBs, I call

files <-list.files(path="C:/Users/fbsmaw/Desktop/Projects/RNC/PyMOLD/key_comparison", pattern=".pdb", full.names=TRUE)
inserting <-pdbaln(files, fit=TRUE)
Reading PDB files:

Error in if (substr(file, 1, 4) == "http") { :
missing value where TRUE/FALSE needed

I have identified which of the three files elicits the error but the message doesn’t suggest how to fix whatever is wrong.

any ideas? I attach the file that causes the issue

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[Xinqiu Yao]

Hi,

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It doesn’t look like a problem of the PDB file. It seems to complain some file name when checking the initial 4 letters. Can you print out the content of the files variable here?

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[Matthew Watson]

Happily, it now suddenly worked. I feel foolish although I can’t see where if anywhere I went wrong before. One thing I did was try full.names =FALSE in the list files step, then =TRUE again and I gave the object a name other than PDBs. After that it worked in the pdbaln step.

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Thanks fr your feedback